Monday, May 24, 2010

Biological Innovations and the Fact of Evolution

Evolutionists insist that evolution is a fact even though there is much debate about how it occurred. But if they debate the question of how evolution occurred, that means it is an open question. And does this not, in turn, mean that whether evolution occurred is also an open question? No, evolutionists assure us, there is no question that evolution occurred—it is a fact—because we observe it occurring. But therein lies the rub:

It is not clear that the mechanisms we observe are capable of causing the origin of species. What we observe are mechanisms that help species to adapt. Whether or not these mechanisms are capable of the larger-scale change evolution requires is in question.

In fact, the scientific evidence suggests that they don’t. So the fact that we observe adaptations is not proof that evolution is a fact. Such a claim amounts to an equivocation on evolution. It could be that the mechanisms we observe are up to the task, but we don’t know that they are.

The question of how evolution occurred is very much relevant to whether evolution occurred. And after centuries of research, we certainly do not know how evolution could have occurred. Here is how one research paper described the problem:

As encompassed by the ‘Synthetic Theory’ (or ‘Modern Synthesis’) of evolutionary biology, the 20th century has provided a thorough understanding of the mechanisms of microevolution (Dobzhansky, 1937; Mayr, 1942; Simpson, 1944; Mayr and Provine, 1980). It is relatively well known how organisms adapt to their environment and, arguably, even how new species originate. However, whether this knowledge suffices to explain macroevolution, narrowly defined here to describe evolutionary processes that bring about fundamental novelties or changes in body plans (Theissen, 2006), has remained highly controversial.

How fundamental innovations (or novelties) originate in evolution remains one of the most enigmatic questions of biology. According to the proponents of the Synthetic Theory, the gradual process of evolution by natural selection that operates within populations and species also creates the unique traits recognizable at higher taxonomic levels, meaning that macroevolution is just microevolution extended over relatively long periods of time.

However, it has been repeatedly pointed out that innovation is different from adaptation, and that the Synthetic Theory, which is largely based on population genetics, falls short of explaining innovations, novelties, and the evolution of body plans (Riedl, 1977; Gilbert et al., 1996; Bateman et al., 1998; Erwin, 2000; Wagner, 2000; Haag and True, 2001; Wagner and Müller, 2002; Wagner and Laubichler, 2004; Müller and Newman, 2005; Theissen, 2006). These are not the only shortcomings of the Synthetic Theory. It considers evolution as the result of changes in allele frequency due to natural selection that engender subtle modifications of phenotype. According to the Synthetic Theory evolution always occurs gradually, in a countless number of almost infinitesimally small steps. Given sufficient time, these gradual changes accumulate and result in the larger differences that typically separate higher taxa. The fossil record, however, with its often abrupt transitions, provides limited evidence for the gradual evolution of new forms (Gould and Eldredge, 1993). In addition, the branching patterns of higher taxa in both animals and plants, as revealed by cladistics, do not support the view that the major features of body plans and their constituent parts arose in a gradual way (Vergara-Silva, 2003).

How fundamental innovations (or novelties) originate in evolution remains one of the most enigmatic questions of biology. But that is the heart of evolution. When evolutionists say evolution is an undeniable fact, they very much are including innovations and novelties. And in doing so, they damage the reputation of science.

Whether or not evolution occurred is another question entirely. But if we want to speak of facts, the fact of the matter is we do not know how, or even whether, evolution occurred. That is a scientific fact, and to claim otherwise is to harm science. Evolutionists accuse skeptics of doing damage to science. If they are genuinely searching for threats to science they should look closer to home.

68 comments:

"Evolutionists insist that evolution is a fact even though there is much debate about how it occurred. But if they debate the question of how evolution occurred, that means it is an open question. And does this not, in turn, mean that whether evolution occurred is also an open question? No, evolutionists assure us, there is no question that evolution occurred—it is a fact—because we observe it occurring. But therein lies the rub."

Let's change a few words and see if the reasoning still holds up:

"Physicists insist that gravitation is a fact even though there is much debate about how it occurs. But if they debate the question of how gravitation occurs, that means it is an open question. And does this not, in turn, mean that whether gravitation occurs is also an open question? No, physicists assure us, there is no question that gravitation occurs—it is a fact—because we observe it occurring. But therein lies the rub."

Absolutely hilarious. First the usual misrepresentation of the state of evolutionary knowledge: "science doesn't know every last detail about evolutionary mechanisms, so it doesn't know anything!!"

...followed by the blatant quote-mining of a scientific paper.

Why did you omit the paragraphs immediately following the ones you quoted? The ones that go on to explain how science's new knowledge of evo-devo filled in many of the unknowns listed?

These shortcomings of the Synthetic Theory in explaining evolutionary novelties led to the reintegration of developmental biology into evolutionary biology, giving rise to the discipline of ‘evolutionary developmental biology’ (‘evo-devo’). The rationale of evo-devo takes into account that multicellular organisms usually develop from single cells (zygotes) in each generation anew. Thus, all evolutionary changes in the morphology of an organism occur by changes in developmental processes. Since development is largely under genetic ‘control’, novel morphological forms in evolution frequently result from changes in so-called ‘developmental control genes’, many of which encode transcription factors. Consequently, evo-devo projects typically study the phylogeny of genes encoding certain classes of transcription factors (such as homeodomain or MADS-domain proteins) and their role in the evolution of morphological features (for further details and discussions of the evo-devo rationale see Gould, 1977; Gilbert et al., 1996; Theissen et al., 2000; Carroll, 2001; Arthur, 2002; Müller and Newman, 2005).

Considerable progress has recently been made in understanding the genetic mechanisms that bring about drastic, yet co-ordinated, changes in the adult phenotype by modification of developmental processes. Changes in both the timing (heterochrony) and the position (heterotopy) of developmental events can occur, although, in the case of plants, they are often difficult to distinguish (Kellogg, 2000). A considerable number of key innovations and characteristics of major clades, most of which have been used as taxonomic characters for decades, can be explained as the result of heterotopy or heterochrony, corroborating the importance of developmental shifts for macroevolution (Kellogg, 2000).

Once again you should be ashamed of yourself, although it's becoming quite apparent you have the standard creationist's total lack of shame for these sort of disgraceful misrepresentations.

"But if they debate the question of how evolution occurred, that means it is an open question. And does this not, in turn, mean that whether evolution occurred is also an open question?"

Odd logic. At a crime scene, we find a murder victim with a gash in the back, no way it is self-inflicted. We question why this occurred, who did it and with what weapon. I don't think I'd question if it happened.

"Whether or not these mechanisms are capable of the larger-scale change evolution requires is in question. In fact, the scientific evidence suggests that they don’t."

According to who? You?

Next, you selectively quoted a nice paper. Following the paragraph summarizing the history of evolution, and how the Synthetic Theory falls short follows:

"These shortcomings of the Synthetic Theory in explaining evolutionary novelties led to the reintegration of developmental biology into evolutionary biology, giving rise to the discipline of ‘evolutionary developmental biology’(‘evo-devo’). The rationale of evo-devo takes intoaccount that multicellular organisms usually develop from single cells (zygotes) in each generation anew. Thus, all evolutionary changes in the morphology of an organism occur by changes in developmental processes. Since developmentis largely under genetic ‘control’, novel morphological forms in evolution frequently result from changes in so-called ‘developmental control genes’, many of which encode transcription factors. Consequently, evodevoprojects typically study the phylogeny of genesencoding certain classes of transcription factors (such as homeodomain or MADS-domain proteins) and their role in the evolution of morphological features (for further details and discussions of the evo-devo rationale see Gould, 1977; Gilbert et al., 1996; Theissen et al., 2000; Carroll,2001; Arthur, 2002; Muller and Newman, 2005)."

"Considerable progress has recently been made in understanding the genetic mechanisms that bring about drastic, yet co-ordinated, changes in the adult phenotype by modification of developmental processes. ... A considerable number of key innovations and characteristics of major clades, most of which have been used as taxonomic characters for decades, can be explained as the result of heterotopy or heterochrony,corroborating the importance of developmental shifts for macroevolution (Kellogg, 2000)"

The paper goes on to describe the developmental genetics of their favorite organism.

Yet another horribly selective quote-mine. How utterly dishonest of you! They present the historical issue, and then the solution that modern science presents, and the empirical data behind it!

And in a post where you included the historical problem, but left out the solution and the data you have the nerve of accusing these scientists of dishonesty and damaging science.

Gary: "The truth is no scientist has any clue at all as to how novel species form."

My my my Gary...ignorant, arrogant, and flat out wrong, all at the same time. It's the creationist hat trick!

Here's a nice overview of speciation for you to read and learn from. Follow with your finger if you have to, be sure to take it out of your nose first. I'd be happy to explain the big words you don't understand.

Gary- You guys are shameless. Do you not understand the papers you mangle in quote-mines, or do you just enjoy it too much to stop?

The context of this quote:

"Reconciling macroevolution with population genetics appears to be a considerable challenge for the future"

Is:

"Due to the large time-scales and diverse mechanisms involved, studying macroevolution is hardly a trivial task. Reconciling macroevolution with population genetics appears to be a considerable challenge for the future (Nutt et al., 2006; Theissen, 2006). The Spe variety of C. bursa-pastoris shows a rare, yet potentially evolutionarily important, phenomenon, specifically the occurrence of a homeotic variety apparently forming stable populations in the wild. A detailed study of the Spe variety may not only tell us more about the developmental genetic mechanisms that generate novel structures in the first place, but also indicate whether, and if so how, drastic morphological variants are established in natural populations."

That is, we've got an ongoing research project. Hefty, but do-able. And the ability to track evolution empirically, by sequencing genes as populations evolve leave you little room to run.

As they say:"What makes Spe so special, however, is its continuous presence in the wild, and hence the fact that both proximate and ultimate causes of evolution can be studied using the same model system."

"Saltation does not fit into contemporary evolutionary theory"

Says who? Ahh-Googling that line brings up only wikipedia. Did you notice the 'citation needed.' Also, you could have kept reading to:

"Polyploidy (most common in plants but not unknown in animals) is considered a type of saltation [2], even though most polyploid individuals are sterile[verification needed]. Polyploidy meets the basic criteria of saltation in that a significant change (in gene numbers) results in speciation in just one generation."

So there are undeniable cases of saltation in evolutionary biology.

"The title "hopeful monster" should have given it away but obviously didn't."

I don't remember Richard Goldscmidt being anti-evolutionary.

Goldschmidt (1933 AAAS address):"the importance of rare but extremely consequential mutations affecting rates of decisive embryonic processes which might give rise to what one might term hopeful monsters, monsters which would start a new evolutionary line if fitting into some empty environmental niche."

This paper argues they have observed exactly this-a rare, but consequential transition. I don't think the exact change has been tracked yet-but this plant has hybridized and is polyploid. The authors also argue homeotic transitions provide a potential mechanism for saltation--where these changes act as the hypothesized macro-mutations, in bringing about large, sudden changes.

Alterations to key genes can do so, because they act as master regulators of whole suites of genes.

We all know the saying: "If the only tool in your toolbox is a hammer, then everything starts to look like a nail."

Just keep hitting that evolution nails into every problem that is presented by new encounters with reality. History has proven that the human race has a propensity for stupid ideas to emerge and be killed by an inability to comport with reality.

It almost sounds heroic how more human resources are going to be wasted on hammering evolution into so many research efforts.

Michael: "It almost sounds heroic how more human resources are going to be wasted on hammering evolution into so many research efforts. "

Tell us Michael, how would you use ID 'theory' to direct valuable research efforts? Say something like predicting the vector transmission pathways for a new viral pathogen? Or use ID 'theory' to do something like an Ames test for measuring the mutagenicity of a bacteria strain? How would you do research into the field of genetic algorithms without using evolutionary models?

Gonna be tough, since there is no actual ID 'theory to draw from, only empty bluster and unsupported speculation.

You forgot 'attempts to discredit the theory of evolution in the vain and futile hope that that makes ID seem more credible' which, as far as I can see, makes up the VAST majority of any 'work' which purports to support ID.

"Is deep homology the covert way of accepting design similarities while diverting attention from the contradictions it pose to evolutionary models that cannot explain the similarities?"

What contradictions? What unexplainable similarities? What are you talking about?

I also always find it hilarious, when pressed with an accomplishment from evolutionary predictions, that you retrospectively claim it is design based work. What a joke. Deep homology is the opposite of design recognition! Design might presume similar designs would be involved in similar functions. Not deep homology-it instead recognizes evolution uses modules by co-opting them for unique functions. This is how yeast cell wall genes reflect on angiogenesis, or plants can model human developmental defects.

Tell you what-you guys make a specific design-based prediction like that, gain undeniable insight into a disease, and shut me up!

Till then, stop the Monday-morning quarterback routine.

RE: Intellectual resources:

The Discover Institute has a $4 million dollar per year budget. Lets say they spend half on research. http://www.baptist2baptist.net/b2barticle.asp?ID=147

NIH grants average $330,000: http://www.nlm.nih.gov/ep/Payplan.html

So, that's about 6 labs worth. I'd say a very average lab might have 2-3 papers a year. So where are the 12-18 peer reviewed articles in mainstream journals? Where's the contribution to medicine?

The experiments aren't bad-they seem reasonably executed, and the authors show creativity in the design. The conclusions are overstated. I'm sure this will be cited as evolution being impossible shortly, and it is not.

Here's why it is actually great proof of evolution in action:

Basically, the authors take a enzyme for Tryptophan (an amino acid) production, with two amino acids in the enzyme mutated to make it non-functional, and query whether, and by what path, it can revert to producing tryptophan.

This is an extension of some classic work where the reversion of a single mutation were studied. In this case, E. coli revert to tryptophan production in the singly mutated case (without mutagenesis) at about 1 per 10^10 clonal colonies.

This study doesn't look at a large enough populations, to get a double reversion--in general, they're well below what would be expected for a single reversion, so (especially in concert with selective antibiotic) the cells are dead without tryptophan. Ok. Asking too much for the screen.

In the presence of a little tryptophan, to keep the cells alive, the cells grow, but never re-evolve tryptophan metabolism. Why? The gross experimental over-expression of thetryptophan synthesizing enzymes is a huge cost for the bacteria. They're spending a ton of energy on it. We see this in recombinant proteinexpression-you can turn bacteria into protein factories, but they're dead by theend. So the cells get by fine with the (relatively abundant) tryptophan provided the media, but the synthetic system forces them to make the enzymes as 15%+ of their total protein. Sick cells.

So, instead, of re-evolving the synthetic machinery, they kick the genes, or mutations inactivating expression are fixed. They just turn it off.

By the authors own data, the inactivating mutations have better fitness in these media conditions, even with the wild type tryptophan enzymes. Again, this is because they over-expressed the target to toxic levels.

And since the bacteria kick expression, to avoid toxicity, they don't evolve tryptophan synthesis.

Its just an inappropriate query for re-evolution of tryptophan synthesis. Dead cells don't evolve. And healthy cells will shut off over-expression that costs them precious resources.

So, evolution worked. The bacteria dodged a worse cost to fitness by shutting down the production of 3 enzymes, and used the tryptophan supplied in the media to survive. In the no tryptophan supplied case, insufficient sampling size (byall known estimates of E. coli mutation rates) means the double mutant had no chance to emerge.

Going forward, I'd be interested in the results with more mild over-expression, more limited tryptophan, and larger numbers screened.

Evolution worked by losing something. It doesn't follow that evolution working by building something can happen. And random changes should gave been able to make the necessary tryptopahn making mutations at least once. Anyway, it is research done by ID'ers.

The E. coli fixed new mutations. We could even call this a gain of suppression of exogenous toxicity. The ablation of a negative thing seems like a positive to me. But, even if we disagree on what to call it, thanks for agreeing that this doesn't falsify evolution. The bacteria adapted in the manner that makes them most fit. In this case, it was by shutting down expression of a parasitic toxic over-expression or protein.

"It doesn't follow that evolution working by building something can happen."

This has been observed many times. Take screens where some critical function of E. coli is ablated. We can then query what second, adaptive change-often a gain of novel function-rescues the first.

For example:A gain-of-function mutation in ftsA bypasses the requirement for the essential cell division gene zipA in Escherichia colihttp://www.pnas.org/content/100/7/4197.full

Not to mention wholesale directed evolution or long-term evolution screens where novel activitieshave been evolved.

"And random changes should gave been able to make the necessary tryptopahn making mutations at least once."

Not in the population size and time allotted. Scooping up a million sardines, placing them on land and asking why they aren't breathing isn't a fair test of evolution of lungs. They, and the bacteria selected with no-tryptophan are equally and immediately dead, and unable to evolve. The ones selected with 'limiting' tryptophan kicked the toxic overexpression of the enzyme, and thrived on the supplied media.

"Anyway, it is research done by ID'ers."

That it is, and I've tried to portray and critique it fairly by presenting their data and conclusions.

Could you please explain the mechanism that achieve this, in layman terms:

"evolution uses modules by co-opting them for unique functions."

It sounds fascinating to hear someone using this language and not even see the semantic relationship to design principles. But I will be educated if you could just explain the evolutionary mechanism that achieve this "co-opting for unique functions".

If you are incapable to see that, ever since the advent of modern genetics, practical research of living systems has become purely driven by a design premises in their efforts, then you just have to stay in your make belief world where Darwin's processes actually did it.

I sincerely pity the poor researchers that are forced to Darwinize their work just to get published. It is like an artist that is forced to frame his work in a toilet seat, every time.

Michael: "If you are incapable to see that, ever since the advent of modern genetics, practical research of living systems has become purely driven by a design premises in their efforts, then you just have to stay in your make belief world where Darwin's processes actually did it.

Another scientifically illiterate goober who doesn't understand that using an analogy as a explanatory framework doesn't mean the analogy is reality.

If you like to call the reality of the design premise in living systems an analogy useful to your Darwinian delusion, that's fine in make belief world. Well done for following Dawkins' example.

To me it is a sign of an incompetent theory.

You actually highlight the absurdity of the evolutionary equivocation.

Since you like analogy so much: "It looks like an apple, it smells like an apple, it tastes like an apple, it has the exact genetic code pattern of an apple... therefore we conclude it is a banana in honor of the Banana King."

Michael: "Could you please explain the mechanism that achieve this, in layman terms:

"evolution uses modules by co-opting them for unique functions."

It sounds fascinating to hear someone using this language and not even see the semantic relationship to design principles. But I will be educated if you could just explain the evolutionary mechanism that achieve this "co-opting for unique functions". "______Sure. Besides conserved pathways where the same players are doing the same thing, other conserved pathways have the same players contributing to a different function. Certain features are abandoned in evolution, as others develop. That we don't make cell walls like yeast or plants opens up an entire linked 'module' to do something else. We might find it participating in blood vessel formation instead. Because of deep homology, these relationships can be recognized.

And again, deep homology is not an ID prediction. You could add it to your long list of retrospective victories, I suppose.

With papers like Theobald's, the recognition of deep homologies, the direct observation of evolution, we're left with acknowledging evolution, or some version of a unevidenced design that was made to look evolved. There's no grand conspiracy of evolutionary biologists who use design inferences, then scrub this from their papers later. We use evolution as a theory because it works.

Let us make some fun with this analogy, for that is the only mechanism you seem to propose (feel free to correct me if I am wrong):

"...conserved pathways where the same players are doing the same thing, other conserved pathways have the same players contributing to a different function"

As a layperson I have to thank you for this vivid & descriptive analogy of the mechanism of evolution that has the capability to "use modules by co-opting them for unique functions".

Leave the players for a while are these pathways extended in the quantum flux where meaningful code has to dance along to become the new computational machine that create unique functions? Was it maybe the Boltzmann Brain that dropped in to impress/mutate the genes/players to follow this path selected for them by their environment?

How many of these paths extend between species that parted evolutionary paths long long ago, even before these unique functions existed with their ancestor? I have to ask because the co-opting that your refer to seems to be between species, the way you presented it.

Oops... it is clear that you have to explain your mechanism and maybe give me more than just so stories/analogies of how you "know" it works.

Let me guess. You've never studies biology, or genetics, probably no science to speak of, and have no clue about the technical topics being discussed in the pertinent papers RobertC keeps providing, right?

I'm not sure what is wrong with what I said, nor what your complaint now is.

I'll refer you to a NYT article by Carl Zimmer. He is more versed in communicating evolution to the public:

http://www.nytimes.com/2010/04/27/science/27gene.html?hp

"The scientists took advantage of a peculiar feature of our evolutionary history. In our distant, amoeba-like ancestors, clusters of genes were already forming to work together on building cell walls and on other very basic tasks essential to life. Many of those genes still work together in those same clusters, over a billion years later, but on different tasks in different organisms."

You just don't get it that I actually do get the good science part in everything you post, it is the Darwinising that is hilarious. Nothing about "deep homology" makes more sense than shared design features in all living organisms across all species. Even the ancestor claims become a mockery as more and more shared gene modules are exposed. But then again, if you only have a hammer everything looks like a nail.

Has anyone tried to calculate and map the consequences of the existence of these shared gene modules on the proposed process that created it in the first place or are thy not really interested in their faith / theory actually making sense. How much gene modules would ultimately have been contained in the most primitive live form to maintain heredity or are we suggesting that the same gene module was randomly created more than one proposed lines of heredity?

There you have my questions, but I suspect you don't really want to answer them because there is no Darwinian answer and you will rather start chanting some Darwinized love song on the beat of real science.

"Nothing about "deep homology" makes more sense than shared design features in all living organisms across all species."

So, presuming the designer altered the design to have different functions in different organisms, and saw fit to use kludges where the same pathway yielding yeast cell walls contributes to blood vessels. It isn't the same design, yielding the same outcome. These are modules that differ, and have been adapted to distinct functions.

Now, along with the phylogenetics, I'd think evolution is the simplest explanation. However, a designer that re-used the same modules, and modified them for distinct function, in a manner that makes them look, by all accounts, evolved--well, that's a fine personal belief, but don't pass it off as science.

I have no idea what you are asking in your second paragraph. Could you rephrase, or split it into separate questions?

How do you detect design in any system, again?How is design distinguished from non-design?

What is the ID explanation for atavistic features, like legs on whales and tails on humans? Was the Designer having an off day and got some modules mixed up? Why do chickens have the genetic component for growing teeth?

I've been asking these questions to ID supporters for almost 5 years now and have never been given a straight answer.

And to the best of my knowledge, the teeth in chickens is caused by the Sonic gene. This gene is found in all vertebrates and controls a lot of aspects of development. It causes teeth to grow teeth when two tissues come together in the mouth. In normal birds these tissues don't come in contact. but in a mutant bird, that dies before birth, they do touch. Please correct me if I'm wrong.

What is the ID explanation for atavistic features, like legs on whales and tails on humans? Was the Designer having an off day and got some modules mixed up? Why do chickens have the genetic component for growing teeth?

I've been asking these questions to ID supporters for almost 5 years now and have never been given a straight answer. "

====Do you want a straight answer or do you want an explination from the designer of His/his/her/its etc. design?

Try to make sense, because your implied claims that these features is best explained by evolution have not even earned the right to be proposed in the first place. There is so many preceding proofs (evidence through proper scientific method that supports a hypothesis) outstanding for evolution that your claims about atavistic features hangs in the air and is not grounded in any evidence.

It is very pertinent speculations for you, but for someone like Behe, that has grounded his view of common descent in ID, these features might just as well be valid proof of common descent.

However if you like to start speculating about design features without knowledge of the intelligence that caused it you are just unscientific and foolish.

natschuster, explanation that claims of organs being some evolutionary remnant has to be verified against current uses. Claiming homology is no evidence that form and function had to be similar in the past. It just forms part of one big self-referential evolutionary argument.

Even though Ritchie did not grasp the consequence of my comment he just blab along about design being impossible to detect - tell that to any science that detect design for their bread and butter (SETI, forensic etc.) and see where it get you. Wake up and realize that design detection is part of every day science. You are actually expected to proof that you did not detect intelligent interference in any natural test programme.

It should NOT read:"However if you like to start speculating about design features without knowledge of the intelligence that caused it you are just unscientific and foolish."

BUT

However if you like to start speculating about the intelligence that caused design features without clear inference to the use / meaning / intent / potential of a specific design, you would be unscientific and foolish.

Even though Ritchie did not grasp the consequence of my comment he just blab along about design being impossible to detect

That is not what I said. I asked you to provide evidence for designed features or this hypotheitcal 'intelligence' which could do the designing. Which you failed to do.

tell that to any science that detect design for their bread and butter (SETI, forensic etc.) and see where it get you.

SETI researcher Seth Shostak has this to say about the comparisson between the techniques used by SETI and those proffered by ID proponents for detecting design:

Well, it's because the credibility of the evidence is not predicated on its complexity. If SETI were to announce that we're not alone because it had detected a signal, it would be on the basis of artificiality. An endless, sinusoidal signal -- a dead simple tone -- is not complex; it's artificial. Such a tone just doesn't seem to be generated by natural astrophysical processes. In addition, and unlike other radio emissions produced by the cosmos, such a signal is devoid of the appendages and inefficiencies nature always seems to add -- for example, DNA's junk and redundancy. (Emphasis in original)

...and...

There's another hallmark of artificiality we consider in SETI, and it's context. Where is the signal found? Our searches often concentrate on nearby Sun-like star systems -- the very type of astronomical locale we believe most likely to harbor Earth-size planets awash in liquid water. That's where we hope to find a signal. The physics of solar systems is that of hot plasmas (stars), cool hydrocarbon gasses (big planets), and cold rock (small planets). These do not produce, so far as we can either theorize or observe, monochromatic radio signals belched into space with powers of ten billion watts or more---the type of signal we look for in SETI experiments. It's hard to imagine how they would do this, and observations confirm that it just doesn't seem to be their thing.

As for forensics, well we don't need to assume the existence of entirely hypothetical (and VASTLY improbable) agents. Human intervention pretty much covers that which forensic experts come up with.

However if you like to start speculating about the intelligence that caused design features without clear inference to the use / meaning / intent / potential of a specific design, you would be unscientific and foolish.

And who is speculating about such things? Notice also that you have smuggled in the phrase 'designed features'. Again, what NATURAL features are designed, exactly?

Thornton: " What is the ID explanation for atavistic features, like legs on whales and tails on humans? Was the Designer having an off day and got some modules mixed up? Why do chickens have the genetic component for growing teeth?

I've been asking these questions to ID supporters for almost 5 years now and have never been given a straight answer."

Michael: "Do you want a straight answer or do you want an explination from the designer of His/his/her/its etc. design? "

I want a straight answer. Not more of the handwaving BS and question avoidance like you just gave. Not excuses, not more attacks on the ToE explanation.

What is the ID explanation for atavistic features?

You claim ID is better able to explain observed phenomena than ToE, well here's your chance. Time to put up or shut up Michael.

Actually, in regard to the SETI researcher's paper, perhaps this would also have been a good paragraph to quote:

In short, the champions of Intelligent Design make two mistakes when they claim that the SETI enterprise is logically similar to their own: First, they assume that we are looking for messages, and judging our discovery on the basis of message content, whether understood or not. In fact, we're on the lookout for very simple signals. That's mostly a technical misunderstanding. But their second assumption, derived from the first, that complexity would imply intelligence, is also wrong. We seek artificiality, which is an organized and optimized signal coming from an astronomical environment from which neither it nor anything like it is either expected or observed: Very modest complexity, found out of context. This is clearly nothing like looking at DNA's chemical makeup and deducing the work of a supernatural biochemist.

Another big point to remember about design detection is that in all know cases the detection rests on pattern matching a previously known design. If forensics or anthropology, archaeologists trying to determine if a stone is a primitive tool or just a random rock try to pattern match it with other known human-produced stone tools. Even SETI is not looking for unknown signal types. It is looking for signal types of the kind known to be generated by humans, on the idea that there are only a finite number of ways to modulate electromagnetic radiation.

Contrast this with ID, which claims to be able to detect design in biological objects without any sort of pattern matching, just by looking at the object itself. But the IDers love to equivocate over the real working method of pattern matching and the complete failure of their own hand-waving failures.

Your insistence that the "atavistic features" has to be an ID research project with the same problem statement as the evolutionary project is misguided. Your issue with these features is the fact that you want to use them as evidence for evolution. There is no logical reason why phenomenon that is considered evidence for one theory (evolution) has to be explained in the same evidentiary framework by another theory.

I hope you can see that ID is not there to take care of the distortions of reality created by the evolutionary hypothesis, ID is there to describe reality.

So stop asking stupid evo-distorted questions and think you have proven ID wrong. It is not an origins question for ID. These features are there and a design hypothesis does not demand it to have significance regarding origins - that's Darwinisms issue.

ID would, for instance, investigate all living features and genetic similarities from a pure information theoretic point of view because it will warrant fare more insight into reality and solve more problems in general as well as questions about origins. Wasting time on using "atavistic features" as proof of your world view is stealing research resources from real world issues.

I have actually read this pathetic misrepresentation of ID by SETI before. Only someone with a grounded fear of losing grant money would concoct such a fantasy.

From you quote:"First, they assume that we are looking for messages, and judging our discovery on the basis of message content, whether understood or not..." (read rest of quote above)

Why pay this much if they are not at least looking for messages and its content?

A more accurate ID method would propose to detect design is by determining if an event is a)highly improbable and b)corresponding to an independently given pattern. (Taken from W.L. Craig's debate with F. Ayala)

This method surely does not chime about complexity at all and would help the SETI very much.

The fact that thy admit that they seek artificiality is more than enough to qualify as design detection. Lastly, what does the "I" in SETI stand for???

Michael: "Your insistence that the "atavistic features" has to be an ID research project with the same problem statement as the evolutionary project is misguided. Your issue with these features is the fact that you want to use them as evidence for evolution. There is no logical reason why phenomenon that is considered evidence for one theory (evolution) has to be explained in the same evidentiary framework by another theory.

Another evasive hand waving non-answer. The whole purpose a theory is to provide an explanation for empirically observed phenomena. Atavisms are empirically observed phenomena. ToE provides a logical, coherent explanation that is supported by the evidence. ID just stands there with its pants around its ankles.

"I hope you can see that ID is not there to take care of the distortions of reality created by the evolutionary hypothesis, ID is there to describe reality"

Atavisms are reality. When will ID start describing why they occur?

"So stop asking stupid evo-distorted questions and think you have proven ID wrong. It is not an origins question for ID. These features are there and a design hypothesis does not demand it to have significance regarding origins - that's Darwinisms issue."

Nah, I think I'll keep asking those embarrassing questions you can't answer. It's fun watching IDers like you bluster and tap-dance, anything to avoid the simple fact that ID has zero explanatory power

Tell us, what good is a 'theory' like ID that can't explain observed reality?

No, my question is like "we have lots of empirical physical evidence that you hit your wife - DNA samples, blood stains , fiber evidence, a surveillance videotape of you hitting her. Do you have an alternative explanation for the overwhelming physical evidence?"

And you refuse to answer. What should the jury think?

"What is the ID explanation for atavisms" is not a loaded question. It's just one you have no answer for.

"A more accurate ID method would propose to detect design is by determining if an event is a)highly improbable and b)corresponding to an independently given pattern."

"Please demonstrate this in action. Who has actually used this method to detect design? Links please."

This was extracted by WL Craig from William Dembski's work "The Design Inference: Eliminating Chance through Small Probabilities" published by "Cambridge Studies in Probability, Induction and Decision Theory".

Let's ignore the point that I asked for a demonstration of this principle in action and you have not given me one, and go straight on to your quote itself.

William Lane Craig is a professional Christian apologist with a doctorate in philosophy and another in theology. In no way is he a scientist. He regularly embarrasses himself thinking up absurd defenses for Christian doctrine.

William Dembski is a mathematician and philopsopher. He is also a professor of philosophy at Southwestern Baptist Theological Seminary in Fort Worth, Texas.

Neither of these people are scientists. Both of these people are fervently religious.

I'd ask for something by someone with a shred of scientific credibility, but that pretty much eliminates everyone in the whole ID movement. The truth is that characters such as Dembski and Craig, who champion religion and are not scientists, pretty much characterises the vast majority of the ID movement.

Yet another clue that ID is an excerise in religious wishful thinking rather than actual SCIENCE?

You would think that "Cambridge Studies in Probability, Induction and Decision Theory" is not a scientific study? Wake up and become part of reality. This is a peer reviewed publication by one of the most prestigious institutions in the mathematical community.

As for suggesting that a philosopher is not qualified to extract an argument from any scientist's work... Philosophy is all about logic and the structure of arguments. That is exactly why I used WL Craig's reference to Dembski's work.

From now I will not waste time on any of your comments that engage in this level of buffoonery.

Dembski's The Design Inference: Eliminating Chance through Small Probabilities was peer reviewed BY PHILOSOPHERS, not biologists.

And no, a philosopher is not qualified do science. That would be like saying a dancer is qualified to sing. They are different disciplines, though they may overlap to a small degree.

The fact remains Dembski is not a scientist. And neither is Craig. In fact, real scientists are rather hard to come by in the ID movement. Funny that.

Philosophy is all about logic and the structure of arguments. That is exactly why I used WL Craig's reference to Dembski's work.

Armchair hypothesizing at best, then. Whichever way you look at it, no evidence as ever found by sitting around and dreaming up arguments! It may help us to come with hypotheses and theories, but not to TEST them - not to come up with actual EVIDENCE. Which is what a scientist does.

From now I will not waste time on any of your comments that engage in this level of buffoonery.

As you choose. But for the record I consider this yet another tactic in your frankly rather embarrassing inability to provide evidence asked of you.

Cornelius G. Hunter is a graduate of the University of Illinois where
he earned a Ph.D. in Biophysics and Computational Biology. He is
Adjunct Professor at Biola University and author of the award-winning Darwin’s God: Evolution and the Problem of Evil. Hunter’s other books include Darwin’s Proof, and his newest book Science’s Blind Spot
(Baker/Brazos Press). Dr. Hunter's interest in the theory of evolution
involves the historical and theological, as well as scientific, aspects
of the theory. His website is http://www.darwins-god.blogspot.com/